[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleStructural insights into ClpP protease side exit pore-opening by a pH drop coupled with substrate hydrolysis.
Journal, issue, pagesEMBO J, Vol. 41, Issue 13, Page e109755, Year 2022
Publish dateJul 4, 2022
AuthorsLeehyeon Kim / Byung-Gil Lee / Minki Kim / Min Kyung Kim / Do Hoon Kwon / Hyunmin Kim / Heike Brötz-Oesterhelt / Soung-Hun Roh / Hyun Kyu Song /
PubMed AbstractThe ClpP serine peptidase is a tetradecameric degradation molecular machine involved in many physiological processes. It becomes a competent ATP-dependent protease when coupled with Clp-ATPases. ...The ClpP serine peptidase is a tetradecameric degradation molecular machine involved in many physiological processes. It becomes a competent ATP-dependent protease when coupled with Clp-ATPases. Small chemical compounds, acyldepsipeptides (ADEPs), are known to cause the dysregulation and activation of ClpP without ATPases and have potential as novel antibiotics. Previously, structural studies of ClpP from various species revealed its structural details, conformational changes, and activation mechanism. Although product release through side exit pores has been proposed, the detailed driving force for product release remains elusive. Herein, we report crystal structures of ClpP from Bacillus subtilis (BsClpP) in unforeseen ADEP-bound states. Cryo-electron microscopy structures of BsClpP revealed various conformational states under different pH conditions. To understand the conformational change required for product release, we investigated the relationship between substrate hydrolysis and the pH-lowering process. The production of hydrolyzed peptides from acidic and basic substrates by proteinase K and BsClpP lowered the pH values. Our data, together with those of previous findings, provide insight into the molecular mechanism of product release by the ClpP self-compartmentalizing protease.
External linksEMBO J / PubMed:35593068 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.79 - 3.4 Å
Structure data

31559

7fep

EMDB-31559, PDB-7fep:
Cryo-EM structure of BsClpP-ADEP1 complex at pH 6.5
Method: EM (single particle) / Resolution: 3.1 Å

31560

7feq

EMDB-31560, PDB-7feq:
Cryo-EM structure of apo BsClpP at pH 6.5
Method: EM (single particle) / Resolution: 3.2 Å

31561

7fer

EMDB-31561, PDB-7fer:
Cryo-EM structure of BsClpP-ADEP1 complex at pH 4.2
Method: EM (single particle) / Resolution: 3.4 Å

31562

7fes

EMDB-31562, PDB-7fes:
Cryo-EM structure of apo BsClpP at pH 4.2
Method: EM (single particle) / Resolution: 3.4 Å

PDB-7p80:
Crystal structure of ClpP from Bacillus subtilis in complex with ADEP2 (compressed state)
Method: X-RAY DIFFRACTION / Resolution: 2.98 Å

PDB-7p81:
Crystal structure of ClpP from Bacillus subtilis in complex with ADEP2 (compact state)
Method: X-RAY DIFFRACTION / Resolution: 2.79 Å

Chemicals

ChemComp-HOH:
WATER / Water

Source
  • bacillus subtilis (bacteria)
  • synthetic construct (others)
  • bacillus subtilis (strain 168) (bacteria)
KeywordsHYDROLASE / ClpP / Bacillus subtilis / ADEP1 / Acyldepsipeptides / ADEP2 / compressed / antibiotics

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more